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   &#160;<span id="projectnumber">2.x</span>
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<div class="PageDoc"><div class="header">
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<div class="title">NINJA Documentation</div>  </div>
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<div class="textblock"><p><a class="anchor" id="md_README"></a><img src="https://github.com/TravisWheelerLab/NINJA/workflows/NINJA%20CI/badge.svg" alt="NINJA CI" style="pointer-events: none;" class="inline"/></p>
<h1><a class="anchor" id="autotoc_md0"></a>
NINJA</h1>
<p>Nearly Infinite Neighbor Joining Application</p>
<h2><a class="anchor" id="autotoc_md1"></a>
About</h2>
<p>TODO: Information from Travis... history, Java version, publication(s)</p>
<h2><a class="anchor" id="autotoc_md2"></a>
Development</h2>
<p>Clone the code. If you're on a Mac, you can run <code>make setup-mac</code> to install most of the required tools through <a href="http://brew.sh">Homebrew</a>. This includes:</p>
<ul>
<li><a href="https://github.com/nickdiego/compiledb">compiledb</a></li>
<li><a href="https://www.doxygen.nl">doxygen</a></li>
<li><a href="https://github.com/pypa/pipenv">pipenv</a></li>
<li>Python 3.8 or greater</li>
</ul>
<p>Contributions are welcomed. To do this, fork the repo, create a branch and, once you're ready, create a pull request from your branch into the <code>master</code> branch in the main repo.</p>
<h2><a class="anchor" id="autotoc_md3"></a>
Authors</h2>
<ul>
<li>Travis Wheeler <a href="#" onclick="location.href='mai'+'lto:'+'tra'+'vi'+'s.w'+'he'+'ele'+'r@'+'umo'+'nt'+'ana'+'.e'+'du'; return false;">travi<span style="display: none;">.nosp@m.</span>s.wh<span style="display: none;">.nosp@m.</span>eeler<span style="display: none;">.nosp@m.</span>@umo<span style="display: none;">.nosp@m.</span>ntana<span style="display: none;">.nosp@m.</span>.edu</a></li>
<li>Michel Wan Der Maas Soares</li>
<li>George Lesica <a href="#" onclick="location.href='mai'+'lto:'+'geo'+'rg'+'e.l'+'es'+'ica'+'@u'+'mon'+'ta'+'na.'+'ed'+'u'; return false;">georg<span style="display: none;">.nosp@m.</span>e.le<span style="display: none;">.nosp@m.</span>sica@<span style="display: none;">.nosp@m.</span>umon<span style="display: none;">.nosp@m.</span>tana.<span style="display: none;">.nosp@m.</span>edu</a> </li>
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